The cobweb of life revealed by genome-scale estimates of horizontal gene transfer

PLoS Biology

Volumn 3, Issue 10, 2005, Pages

  Ge, Fan ^a   Wang, Li San ^a   Kim, Junhyong ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPARATIVE STUDY; DATA BASE; GENE CLUSTER; HORIZONTAL GENE TRANSFER; MICROBIAL GENETICS; ORTHOLOGY; PHYLOGENY; QUANTITATIVE ANALYSIS; STATISTICAL MODEL; STATISTICAL SIGNIFICANCE; ALGORITHM; BACTERIAL GENOME; BIOLOGICAL MODEL; BIOLOGY; GENETICS; GENOME; MOLECULAR EVOLUTION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME; GENOME, ARCHAEAL; GENOME, BACTERIAL; GENOME, FUNGAL; MODELS, GENETIC;

EID: 26444580130     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0030316     Document Type: Article

References (58)

1. Brown JR (2003) Ancient horizontal gene transfer. Nat Rev Genet 4: 121-132.
2. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, et al. (1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399: 323-329.
3. Koonin EV, Makarova KS, Aravind L (2001) Horizontal gene transfer in prokaryotes: Quantification and classification. Annu Rev Microbiol 55: 709-742.
4. Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19: 2226-2238.
5. Martin W, Stoebe B, Goremykin V, Hapsmann S, Hasegawa M, et al. (1998) Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393: 162-165.
6. Huang CY, Ayliffe MA, Timmis JN (2003) Direct measurement of the transfer rate of chloroplast DNA into the nucleus. Nature 422: 72-76.
7. Bergthorsson U, Adams KL, Thomason B, Palmer JD (2003) Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: 197-201.
8. Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY, Blankenship RE (2002) Whole-genome analysis of photosynthetic prokaryotes. Science 298: 1616-1620.
9. Andersson JO, Sjogren AM, Davis LA, Embley TM, Roger AJ (2003) Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr Biol 13: 94-104.
10. Woese CR, Olsen GJ, Ibba M, Soll D (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev 64: 202-236.
11. Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284: 2124-2129.
12. Nesbo CL, Boucher Y, Doolittle WF (2001) Defining the core of nontransferable prokaryotic genes: The euryarchaeal core. J Mol Evol 53: 340-350.
13. Woese CR (2002) On the evolution of cells. Proc Natl Acad Sci U S A 99: 8742-8747.
14. Kurland CG, Canback B, Berg OG (2003) Horizontal gene transfer: A critical view. Proc Natl Acad Sci U S A 100: 9658-9662.
15. Philippe H, Douady CJ (2003) Horizontal gene transfer and phylogenetics. Curr Opin Microbiol 6: 498-505.
16. Lawrence JG, Ochman H (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A 95: 9413-9417.
17. Nakamura Y, Itoh T, Matsuda H, Gojobori T (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36: 760-766.
18. Olendzenski L, Liu L, Zhaxybayeva O, Murphey R, Shin DG, et al. (2000) Horizontal transfer of archaeal genes into the deinococcaceae: Detection by molecular and computer-based approaches. J Mol Evol 51: 587-599.
19. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304.
20. Garcia-Vallve S, Romeu A, Palau J (2000) Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res 10: 1719-1725.
21. Klenk HP, Meier TD, Durovic P, Schwass V, Lottspeich F, et al. (1999) RNA polymerase of Aquifex pyrophilus: Implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria. J Mol Evol 48: 528-541.
22. Bapteste E, Boucher Y, Leigh J, Doolittle WF (2004) Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol 12: 406-411.
23. Ragan MA (2001) On surrogate methods for detecting lateral gene transfer. FEMS Microbiol Lett 201: 187-191.
24. Jain R, Rivera MC, Lake JA (1999) Horizontal gene transfer among genomes: The complexity hypothesis. Proc Natl Acad Sci U S A 96: 3801-3806.
25. Eisen JA (2000) Horizontal gene transfer among microbial genomes: New insights from complete genome analysis. Curr Opin Genet Dev 10: 606-611.
26. Matte-Tailliez O, Brochier C, Forterre P, Philippe H (2002) Archaeal phylogeny based on ribosomal proteins. Mol Biol Evol 19: 631-639.
27. Daubin V, Gouy M, Perriere G (2002) A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history. Genome Res 12: 1080-1090.
28. Lerat E, Daubin V, Moran NA (2003) >From gene trees to organismal phylogeny in prokaryotes: The case of the γ-Proteobacteria. PLoS Biol 1: e19. DOI: 10.1371/journal.pbio.0000019
29. Dutilh BE, Huynen MA, Bruno WJ, Snel B (2004) The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J Mol Evol 58: 527-539.
30. Daubin V, Ochman H (2004) Quartet mapping and the extent of lateral transfer in bacterial genomes. Mol Biol Evol 21: 86-89.
31. Kyrpides NC, Olsen GJ (1999) Archaeal and bacterial hyperthermophiles: Horizontal gene exchange or common ancestry? Trends Genet 15: 298-299.
32. Maddison WP (1997) Gene trees in species trees. Syst Biol 46: 523-526.
33. Slowinski JB, Page RD. (1999) How should species phylogenies be inferred from sequence data? Syst Biol 48: 814-825.
34. Kim J, Salisbury BA (2001) A tree obscured by vines: Horizontal gene transfer and the median tree method of estimating species phylogeny. Pac Symp Biocomput 6: 571-582.
35. Novichkov PS, Omelchenko MV, Gelfand MS, Mironov AA, Wolf YI, et al. (2004) Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol 186: 6575-6585.
36. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, et al. (2001) The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29: 22-28.
37. Brochier C, Philippe H (2002) Phylogeny: A non-hyperthermophilic ancestor for bacteria. Nature 417: 244.
38. Gupta RS, Griffiths E (2002) Critical issues in bacterial phylogeny. Theor Popul Biol 61: 423-434.
39. Griffiths E, Gupta RS (2004) Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquificales. Int Microbiol 7: 41-52.
40. Iyer LM, Koonin EV, Aravind L (2004) Evolution of bacterial RNA polymerase: Implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 335: 73-88.
41. Cavalier-Smith T (2002) The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 52: 7-76.
42. Brochier C, Forterre P, Gribaldo S (2004) Archaeal phylogeny based on proteins of the transcription and translation machineries: Tackling the Methanopyrus kandleri paradox. Genome Biol 5: R17.
43. Kennedy SP, Ng WV, Salzberg SL, Hood L, DasSarma S (2001) Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res 11: 1641-1650.
44. Goddard W, Kubicka E, Kubicki G, McMorris FR (1994) The agreement metric for labeled binary trees. Math Biosci 123: 215-226.
45. Robinson DF, Foulds LR (1981) Comparison of phylogenetic trees. Math Biosci 53: 131-147.
46. Conover WJ (1999) Practical nonparametric statistics, 3rd ed. New York: Wiley. 584 p.
47. Harris JK, Kelley ST, Spiegelman GB, Pace NR (2003) The genetic core of the universal ancestor. Genome Res 13: 407-412.
48. Dufraigne C, Fertil B, Lespinats S, Giron A, Deschavanne P (2005) Detection and characterization of horizontal transfers in prokaryotes using genomic signature. Nucleic Acids Res 33(1): e6. Available: http://www. pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15653627. Accessed 19 July 2005.
49. Medrano-Soto A, Moreno-Hagelsieb G, Vinuesa P, Christen JA, Collado-Vides J (2004) Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes. Mol Biol Evol 21: 1884-1894.
50. Ortutay C, Gaspari Z, Toth G, Jager E, Vida G, et al. (2003) Speciation in Chlamydia: Genomewide phylogenetic analyses identified a reliable set of acquired genes. J Mol Evol 57: 672-680.
51. Daubin V, Moran NA, Ochman H (2003) Phylogenetics and the cohesion of bacterial genomes. Science 301: 829-832.
52. Lawrence JG, Hendrickson H (2003) Lateral gene transfer: When will adolescence end? Mol Microbiol 50: 739-749.
53. Salzberg SL, White O, Peterson J, Eisen JA (2001) Microbial genes in the human genome: Lateral transfer or gene loss? Science 292: 1903-1906.
54. Snel B, Bork P, Huynen MA (2002) Genomes in flux: The evolution of archaeal and proteobacterial gene content. Genome Res 12: 17-25.
55. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
56. Felsenstein J (1993) PHYLIP (Phylogeny Inference Package), version 3.5c [computer program]. Seattle: University of Washington Department of Genetics. Available: http://evolution.genetics.washington.edu/phylip.html. Accessed 19 July 2005.
57. Swofford DL (2002) PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4 [computer program]. Sunderland (Massachusetts): Sinauer.
58. Semple C, Steel M (2003) Phylogenetics. New York: Oxford University Press. 239 p.